Genetic diversity of Thymus daenensis subsp. daenensis using SRAP markers

Biologia ◽  
2015 ◽  
Vol 70 (4) ◽  
Author(s):  
Majid Talebi ◽  
Mehdi Rahimmalek ◽  
Mohsen Norouzi
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Pollen Dispersal ◽  
Distribution Area ◽  
Zagros Mountains ◽  
Breeding Programs ◽  
Srap Markers ◽  
Central Regions ◽  
Limited Gene Flow ◽  
Zagros Range

AbstractThymus daenensis subsp. daenensis is an aromatic medicinal plant endemic to Iran and generally grows in high altitudes in Zagros Mountains range. Molecular markers provide valuable information about relative genetic relationships for facilitate breeding programs. Here, we used SRAP markers to estimate the genetic diversity of 79 T. daenensis accessions from 16 regions in Iran, located at extremes and the central regions of the Zagros range. Fourteen SRAP primer combinations (PCs) amplified 240 stable and reproducible fragments, of which 198 (82.5%) were polymorphic for all accessions. The PIC value for PCs ranged from 0.195 to 0.333 with an average of 0.284. Neighbor-joining tree constructed from Dice’s similarity matrix of SRAP data revealed two major groups and verified with the results of AMOVA (P < 0.001; genetic distance = 0.98). The Tc and Te groups included the accessions collected from the center and the extremes of the Zagros Mountains, respectively. The results showed that the current scattered distribution area of Iranian thyme is probably recent due mainly to anthropic pressures and limited gene flow via seed and/or pollen dispersal.

scholarly journals Population structure and phylogenetic relationships in Brassica rapa L. subspecies by using isozyme markers

2020 ◽  
Author(s):  
R. H. Sammour ◽  
M. A. Karam ◽  
Y. S. Morsi ◽  
R. M. Ali
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Brassica Rapa ◽  
Phylogenetic Relationships ◽  
Fixation Index ◽  
Distribution Area ◽  
Enzyme Analysis ◽  
Breeding Programs ◽  
Expected Heterozygosity ◽  
Wide Range

Abstract The present study aimed to assess population structure and phylogenetic relationships of nine subspecies of Brassica rapa L. represented with thirty-five accessions cover a wide range of species distribution area using isozyme analysis in order to select more diverse accessions as supplementary resources that can be utilized for improvement of B. napus. Enzyme analysis resulted in detecting 14 putative polymorphic loci with 27 alleles. Mean allele frequency 0.04 (rare alleles) was observed in Cat4A and Cat4B in sub species Oleifera accession CR 2204/79 and in subspecies trilocularis accessions CR 2215/88 and CR 2244/88. The highest genetic diversity measures were observed in subspecies dichotoma, accession CR 1585/96 (the highest average of observed (H0) and expected heterozygosity (He), and number of alleles per locus (Ae)). These observations make this accession valuable genetic resource to be included in breeding programs for the improvement of oilseed B. napus. The average fixation index (F) is significantly higher than zero for the analysis accessions indicating a significant deficiency of heteozygosity. The divergence among subspecies indicated very great genetic differentiation (FST = 0.8972) which means that about 90% of genetic diversity is distributed among subspecies, while 10% of the diversity is distributed within subspecies. This coincides with low value of gene flow (Nm = 0.0287). B. rapa ssp. oleifera (turnip rape) and B. rapa ssp. trilocularis (sarson) were grouped under one cluster which coincides with the morphological classification.

scholarly journals Genetic Diversity Analysis of Sugarcane Parents in Chinese Breeding Programmes Using gSSR Markers

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Qian You ◽  
Liping Xu ◽  
Yifeng Zheng ◽  
Youxiong Que
Keyword(s):  
Genetic Diversity ◽  
Molecular Diversity ◽  
Genetic Relationships ◽  
Breeding Programs ◽  
Sugarcane Varieties ◽  
Breeding Station ◽  
The World ◽  
Breeding Programmes ◽  
Genetic Structures ◽  
Simple Sequence

Sugarcane is the most important sugar and bioenergy crop in the world. The selection and combination of parents for crossing rely on an understanding of their genetic structures and molecular diversity. In the present study, 115 sugarcane genotypes used for parental crossing were genotyped based on five genomic simple sequence repeat marker (gSSR) loci and 88 polymorphic alleles of loci (100%) as detected by capillary electrophoresis. The values of genetic diversity parameters across the populations indicate that the genetic variation intrapopulation (90.5%) was much larger than that of interpopulation (9.5%). Cluster analysis revealed that there were three groups termed as groups I, II, and III within the 115 genotypes. The genotypes released by each breeding programme showed closer genetic relationships, except the YC series released by Hainan sugarcane breeding station. Using principle component analysis (PCA), the first and second principal components accounted for a cumulative 76% of the total variances, in which 43% were for common parents and 33% were for new parents, respectively. The knowledge obtained in this study should be useful to future breeding programs for increasing genetic diversity of sugarcane varieties and cultivars to meet the demand of sugarcane cultivation for sugar and bioenergy use.

scholarly journals (1) Genetic Diversity of Cowpea [Vigna unguiculata (L.) Walp.] Breeding Lines from Different Countries Determined by AFLP Markers

HortScience ◽  
2005 ◽  
Vol 40 (4) ◽  
pp. 998A-998 ◽  
Author(s):  
Jinggui Fang ◽  
Panchanoor S. Devanand ◽  
Chih Cheng T. Chao ◽  
Philip A. Roberts ◽  
Jeff D. Ehlers
Keyword(s):  
Genetic Diversity ◽  
South America ◽  
Near Infrared ◽  
Genetic Relationships ◽  
The United States ◽  
Aflp Markers ◽  
Sub Saharan Africa ◽  
Breeding Programs ◽  
Breeding Lines

Cowpea (2n=2x=22) is a high protein, short-cycle, and essential legume food crop of the tropics, especially in the low input agricultural areas of sub-Saharan Africa, Asia, and South America. Lack of genetic diversity within breeding programs can limit long-term gains from selection. The cowpea gene pool is thought to be narrow and the genetic diversity within breeding programs could be even less diverse. Genetic relationships among 87 cowpea accessions, including 60 advanced breeding lines from six breeding programs in Africa and the United States, and 27 accessions from Africa, Asia, and South America were examined using amplified fragment length polymorphism (AFLP) markers with six near-infrared fluorescence labeled EcoR I + 3/Mse I + 3 primer sets. A total of 382 bands were scored among the accessions with 207 polymorphic bands (54.2%). Overall, the 87 cowpea accessions have narrow genetic basis and they shared minimum 86% genetic similarities. The data also show that the advanced breeding lines of different programs have higher genetic affinities with lines from the same program but not with lines from other programs. The results suggest that there is a need to incorporate additional germplasm of different genetic background into these breeding lines and to ensure the long-term genetic gains of the programs.

Evaluation of Genetic Diversity of Local-Colored Rice Landraces Using SSR Markers

2018 ◽  
Vol 67 ◽  
pp. 24-34 ◽  
Author(s):  
Hoang Thi Hue ◽  
La Tuan Nghia ◽  
Hoang Tuyet Minh ◽  
La Hoang Anh ◽  
Le Thi Thu Trang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genetic Relationships ◽  
Germplasm Conservation ◽  
Similarity Coefficients ◽  
Breeding Programs ◽  
Rice Landraces ◽  
Local Germplasm ◽  
Rice Improvement ◽  
Colored Rice

Analysis of genetic diversity of 90 Vietnamese local-colored rice accessions was evaluated by using 40 SSR markers. The numbers of polymorphic alleles ranged from 3 to 12 alleles per locus and average of 7.1 alleles per locus. The similarity coefficients of the rice landraces fluctuated from 0.76 to 0.93; at a genetic correlation level of 0.78. Ninety accessions of rice landraces were divided into five groups based on analysis of genetic relationships. The results have indicated that 11 markers included: M250, RM302, RM10926, RM208, RM227, RM17231, RM23251, RM5647, RM1376, RM339 and RM228 which gave the unique allele. These markers can be used effectively for genetic diversity of colored rice and provided a specific database and useful materials for landraces identification, local germplasm conservation for further colored rice improvement on rice quality via rice breeding programs in Vietnam.

Genetic diversity and relationships among Dutch elm disease tolerant Ulmus pumila L. accessions from China

Genome ◽  
2008 ◽  
Vol 51 (7) ◽  
pp. 492-500 ◽  
Author(s):  
Juan E. Zalapa ◽  
Johanne Brunet ◽  
Raymond P. Guries
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Genetic Relationships ◽  
Dutch Elm Disease ◽  
Ulmus Pumila ◽  
Breeding Programs ◽  
Republic Of China ◽  
Diversity Assessment ◽  
Diversity Estimates ◽  
Regional Gene

Elm breeding programs worldwide have relied heavily on Asian elm germplasm, particularly Ulmus pumila , for the breeding of Dutch elm disease tolerant cultivars. However, the extent and patterning of genetic variation in Asian elm species is unknown. Therefore, the objective of this research was to determine the extent of genetic diversity among 53 U. pumila accessions collected throughout the People’s Republic of China. Using 23 microsatellite loci recently developed in the genus Ulmus , a total of 94 alleles were identified in 15 polymorphic and 4 monomorphic loci. The average number of alleles per locus was 4.9, with a range of 1–11 alleles. Gene diversity estimates per locus ranged from 0.08 to 0.87, and the non-exclusion probability for the 15 polymorphic loci combined was 0.7 × 10−9. Nineteen region-specific alleles were identified, and regional gene diversity estimates were moderately high (0.48–0.57). The genetic relationships among accessions and regions were estimated by UPGMA and principal coordinate analysis. Both techniques discriminated all accessions and regions. Two microsatellite markers (UR175 + UR123 or Ulm-3) were sufficient to discriminate up to 99.7% of the accessions studied. This research provides useful information for DNA-based fingerprinting, breeding, ecological studies, and diversity assessment of elm germplasm.

scholarly journals SNP-Based Genotyping Provides Insight Into the West Asian Origin of Russian Local Goats

2021 ◽  
Vol 12 ◽  
Author(s):  
Tatiana E. Deniskova ◽  
Arsen V. Dotsev ◽  
Marina I. Selionova ◽  
Henry Reyer ◽  
Johann Sölkner ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Principal Component ◽  
Production Traits ◽  
Effective Population ◽  
Altai Mountain ◽  
Asian Origin ◽  
Breeding Programs ◽  
Population Sizes ◽  
High Level

Specific local environmental and sociocultural conditions have led to the creation of various goat populations in Russia. National goat diversity includes breeds that have been selected for down and mohair production traits as well as versatile local breeds for which pastoralism is the main management system. Effective preservation and breeding programs for local goat breeds are missing due to the lack of DNA-based data. In this work, we analyzed the genetic diversity and population structure of Russian local goats, including Altai Mountain, Altai White Downy, Dagestan Downy, Dagestan Local, Karachaev, Orenburg, and Soviet Mohair goats, which were genotyped with the Illumina Goat SNP50 BeadChip. In addition, we addressed genetic relationships between local and global goat populations obtained from the AdaptMap project. Russian goats showed a high level of genetic diversity. Although a decrease in historical effective population sizes was revealed, the recent effective population sizes estimated for three generations ago were larger than 100 in all studied populations. The mean runs of homozygosity (ROH) lengths ranged from 79.42 to 183.94 Mb, and the average ROH number varied from 18 to 41. Short ROH segments (&lt;2 Mb) were predominant in all breeds, while the longest ROH class (&gt;16 Mb) was the least frequent. Principal component analysis, Neighbor-Net graph, and Admixture clustering revealed several patterns in Russian local goats. First, a separation of the Karachaev breed from other populations was observed. Moreover, genetic connections between the Orenburg and Altai Mountain breeds were suggested and the Dagestan breeds were found to be admixed with the Soviet Mohair breed. Neighbor-Net analysis and clustering of local and global breeds demonstrated the close genetic relations between Russian local and Turkish breeds that probably resulted from past admixture events through postdomestication routes. Our findings contribute to the understanding of the genetic relationships of goats originating in West Asia and Eurasia and may be used to design breeding programs for local goats to ensure their effective conservation and proper management.

scholarly journals Application of Sequence-related Amplified Polymorphism Markers for Characterization of Turfgrass Species

HortScience ◽  
2004 ◽  
Vol 39 (5) ◽  
pp. 955-958 ◽  
Author(s):  
H. Budak ◽  
R.C. Shearman ◽  
R.E. Gaussoin ◽  
I. Dweikat
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Warm Season ◽  
Italian Ryegrass ◽  
Cool Season ◽  
Srap Markers ◽  
Phenetic Relationships ◽  
Wide Range ◽  
Close Relationship

A simple marker technique called sequence-related amplified polymorphism (SRAP) provides a useful tool for estimation of genetic diversity and phenetic relationships in natural and domesticated populations. Previous studies and our initial screen showed SRAP is highly polymorphic and more informative when compared to AFLP, RAPD and SSR markers. In this study, applicability of the SRAP markers to obtain an overview of genetic diversity and phenetic relationships present among cool-season (C3) and warm-season (C4) turfgrass species and their relationship with other Gramineae species were tested. Phenetic trees based on genetic similarities (UPGMA, N-J) were consistent with known taxonomic relationships. In some cases, well-supported relationships as well as evidence by genetic reticulation could be inferred. There was widespread genetic variation among C3 and C4 turfgrass species. In Dice based cophenetic matrix, genetic similarities among all species studied ranged from 0.08 to 0.94, whereas in Jaccard based cophenetic matrix, genetic similarities ranged from 0.05 to 0.85. C3 and C4 species were clearly distinguishable and a close relationship between italian ryegrass and tall fescue were obtained based on SRAP. Genome structures of turfgrasses are comparable to other Gramineae species. This research indicates that the SRAP markers are useful for estimating genetic relationships in a wide range of turfgrass species. The SRAP markers identified in this study can provide a useful reference for future turfgrass breeding efforts.

scholarly journals Genetic diversity and genetic relationships in Hyacinthaceae in India using RAPD and SRAP markers

2013 ◽  
Vol 20 (1) ◽  
pp. 103-114 ◽  
Author(s):  
Tabassum Jehan ◽  
Amit Vashishtha ◽  
S. R. Yadav ◽  
Suman Lakhanpaul
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Srap Markers

scholarly journals Evaluation of Molecular and Morphological Diversity of Capparis Spinosa

2021 ◽  
Author(s):  
Noshin Mahmodi ◽  
Gholam-Reza Sharifi-Sirchi ◽  
Kianoosh Cheghamirza
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Relationships ◽  
Perfect Match ◽  
Morphological Diversity ◽  
Issr Markers ◽  
Zagros Mountains ◽  
Geographical Regions ◽  
Capparis Spinosa ◽  
Polymorphic Bands

Abstract The objective of this study was the evaluation of molecular and morphological diversity among 80 caper (Capparis spinosa L.) genotypes from the 12 regions of the central Zagros Mountains located in the west of Iran. The results showed a high level of morphological genetic variation among the caper samples. According to the morphological cluster analysis, 80 genotypes were clustered into five main groups. The 15 factors justified 78.7 % of the total variation based on factor analysis. ISSR primers produced a total of 108 polymorphic bands (85.04%) from 127 bands and the PIC for primers ranged from 0.01 to 0.52. SCoT primers produced a total of 165 polymorphic bands (86.84%) from 190 bands and the PIC for primers ranged from 0.06 to 0.55. Ordination and cluster analysis by ISSR markers showed that the genetic relationships among all accessions could be separated into three major groups and by SCoT markers separated into six groups. The results did not show a perfect match between the molecular diversity groupings and geographical regions, because many natural factors and human activities shape the amount and pattern of genetic diversity in a plant population. SCoT markers were more informative than ISSR markers for the assessment of genetic diversity of caper germplasm. The combined (ISSR+SCoT) markers haven't shown more information of genetic diversity than single analysis of ISSR and SCoT. The results indicated the existence of dispersion and different levels of morphological variation and molecular genetic diversity in the genotypes collected from west of Iran.

Genetic Diversity and Relationships of 24 Strains of Genus Auricularia (Agaricomycetes) Assessed Using SRAP Markers

2016 ◽  
Vol 18 (10) ◽  
pp. 945-954
Author(s):  
Ping Du ◽  
Tian-Xu Cao ◽  
Bao-Kai Cui ◽  
Yuan Yuan ◽  
Yu-Cheng Dai
Keyword(s):  
Genetic Diversity ◽  
Srap Markers
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